Contacts of the strand formed by residues 533 - 539 (chain B) in PDB entry 2PMW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 533 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ALA* 1.3 80.5 - - - +
534B CYS* 1.3 59.7 + - - +
535B SER* 5.3 0.2 + - - -
557B HIS* 4.8 2.8 + - - +
600B CYS 4.1 0.3 - - - +
601B CYS* 3.4 0.2 - - - -
602B HIS* 2.7 58.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B GLU* 3.9 23.9 + - - +
483B LEU 5.5 2.2 - - - +
484B LEU* 3.9 11.0 - - + -
507B LEU* 5.1 10.8 - - + +
529B LEU* 4.5 0.7 - - - -
532B ALA* 4.0 15.1 + - - -
533B ASN* 1.3 75.9 - - - +
535B SER* 1.3 66.7 + - - +
599B SER* 5.0 4.0 - - - +
600B CYS 3.1 5.6 - - - +
601B CYS* 2.0 46.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 4.6 8.5 - - - +
533B ASN 5.3 0.2 + - - -
534B CYS* 1.3 79.0 - - - +
536B VAL* 1.3 66.2 - - - +
537B HIS* 3.9 16.2 + - - -
554B GLN* 5.2 5.2 + - - -
557B HIS* 5.3 2.9 - - - -
599B SER* 3.6 4.5 + - - -
600B CYS* 2.7 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B MET* 3.8 40.4 - - + +
507B LEU* 3.9 27.9 - - + +
535B SER* 1.3 79.8 - - - +
537B HIS* 1.3 73.5 + - - +
538B THR* 3.7 20.3 + - - +
597B HIS* 4.2 13.0 - - + -
598B ALA 3.2 11.0 - - - +
599B SER* 4.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B SER* 3.9 15.4 + - - -
536B VAL* 1.3 81.1 - - - +
538B THR* 1.3 61.2 + - - +
550B VAL* 3.8 20.4 - - + +
551B HIS 3.5 14.6 + - - +
552B CYS* 4.1 13.5 - - + -
553B HIS* 3.4 36.8 + + - -
554B GLN* 4.7 9.9 + - - -
596B ILE 3.7 0.9 - - - +
597B HIS* 3.3 2.9 - - - -
598B ALA* 2.8 43.3 + - + +
600B CYS* 3.7 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B MET 5.4 0.3 + - - -
536B VAL* 3.7 11.5 + - - +
537B HIS* 1.3 77.5 - - - +
539B ALA* 1.3 73.2 + - - +
540B PRO* 4.3 4.6 - - + +
550B VAL* 4.4 4.6 - - - +
595B SER* 4.8 2.7 - - - -
596B ILE 3.2 4.0 - - - +
597B HIS* 2.8 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B HIS 4.4 0.2 + - - -
538B THR* 1.3 78.3 - - - +
540B PRO* 1.3 70.4 - - + +
548B THR* 3.6 5.9 - - + +
549B ARG 3.5 25.1 - - - +
550B VAL* 4.1 5.8 - - + +
595B SER* 3.2 2.9 - - - -
596B ILE* 2.8 41.9 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il